# HG changeset patch
# User earlhaminst
# Date 1740395216 0
# Node ID a6c4483a02be1130534595010a0f2df1c57f42f3
# Parent  b9f1bcf5ee599ebd3d0a2aa44ff7678ecf860df6
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA/ commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty

diff -r b9f1bcf5ee59 -r a6c4483a02be GAFA.xml
--- a/GAFA.xml	Wed Apr 25 10:59:55 2018 -0400
+++ b/GAFA.xml	Mon Feb 24 11:06:56 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="gafa" name="Gene Align and Family Aggregator" version="0.3.0">
+<tool id="gafa" name="Gene Align and Family Aggregator" version="0.3.1">
     <description>generates an SQLite database that can be visualised with Aequatus</description>
     <command detect_errors="exit_code">
 <![CDATA[
@@ -14,7 +14,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="treeFile" type="data" format="nhx" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" />
+        <param name="treeFile" type="data" format="nhx,newick" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" />
         <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" />
         <param name="genesFile" type="data" format="sqlite" label="Gene features" help="Gene features in SQLite format generated by 'GSTF preparation' tool" />
     </inputs>
@@ -37,9 +37,10 @@
 
 N.B.: The tool will modify the sequence identifiers found in the "Protein alignments" dataset by removing everything from the first underscore to the end of the string.
 
-.. _Aequatus: http://aequatus.earlham.ac.uk
+.. _Aequatus: https://github.com/TGAC/Aequatus
 ]]>
     </help>
     <citations>
+        <citation type="doi">https://doi.org/10.1093/gigascience/giy005</citation>
     </citations>
 </tool>